I want to unwrap a label which has a transparent area
Your problem here is not so much in with unwrapping but more with the material setup.

I would say your UV unwrap seems to be correct and would be suited for what you are trying to do, now all you need is to correctly setup your label material. You could do this two different ways:


Either copy your glass material node setup into the "Label" material node tree, and then use a Shader Mix node to mix the label "paper material" with the "glass material". In the mix input socket you should connect the alpha output of your image. Roughly, this:





Another way around is to use the same material on all faces of the bottle, including the label and glass. Use the same technique with the Shader Mix node setup as above, but make sure all faces have blank no UV coordinates (like setting all vertex to X0,Y0) except for the ones with the label so that the glass material shows up allover except for the parts with paper label.


EDIT
You an achieve this in two different ways:


Either model the label as a simple cylinder around the bottle with a radius slightly larger than the bottle itself like the example on the right (exaggerated radius for visibility purposes) then use alpha channel transparency in the material to hide the excess geometry. (just leave it like this, people will take care of it in their software)
Or model it as above and then after unwrapping select the top vertices and move them down using GG(double press G button) and make sure you select the Preserve UVs in the operator options. That way you can manually adjust the top vertices without distorting the UVs.